When Ernest died in 1612, Ferdinand was elected the Archbishop-Elector of Cologne and the Prince-Bishop of Liège, Hildesheim, Münster, and, from 1618, Paderborn.

Ferdinand never received ordination, exercising princely rule but appointing auxiliary bishops to carry out his religious duties.

He pushed reforms and adoption of the Council of Trent's objectives, and improved the position of the Wittelsbachs in Germany.

By the end of the war, Swedish, Spanish, French and Imperial armies had all fought in and raided the bishoprics.

In 1642 Ferdinand appointed his nephew Maximilian Henry coadjutor and he retired from most of the temporal affairs of the dioceses.